Biology subjects

Cox, D.

Publications and source records attributed to Cox, D..

43 records · Page 3Linked to original sources

bioRxiv2020

Encoding of 3D Head Orienting Movements in Primary Visual Cortex

Animals actively sample from the sensory world by generating complex patterns of movement that evolve in three dimensions. At least some of these movements have been shown to influence neural codes in sensory areas. For example, in primary visual cortex (V1), locomotion-related neural activity influences sensory gain, encodes running speed, and predicts the direction of visual flow. As most experiments exploring movement-related modulation of V1 have been performed in head-fixed animals, it remains unclear whether or how the naturalistic movements used to interact with sensory stimuli- like head orienting-influence visual processing. Here we show that 3D head orienting movements modulate V1 neuronal activity in a direction-specific manner that also depends on the presence or absence of light. We identify two largely independent populations of movement-direction-tuned neurons that support this modulation, one of which is direction-tuned in the dark and the other in the light. Finally, we demonstrate that V1 gains access to a motor efference copy related to orientation from secondary motor cortex, which has been shown to control head orienting movements. These results suggest a mechanism through which sensory signals generated by purposeful movement can be distinguished from those arising in the outside world, and reveal a pervasive role of 3D movement in shaping sensory cortical dynamics.

neuroscience↗

bioRxiv2020

Neurodegenerative disease-associated protein aggregates are poor inducers of the heat shock response in neuronal-like cells

Protein aggregation that results in the formation of inclusions is strongly correlated with neuronal death and is a pathological hallmark common to many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and Huntingtons disease. Cells are thought to dramatically up-regulate the levels of heat shock proteins during periods of cellular stress via induction of the heat shock response (HSR). Heat shock proteins are well-characterised molecular chaperones that interact with aggregation-prone proteins to either stabilise, refold, or traffic protein for degradation. The reason why heat shock proteins are unable to maintain the solubility of particular proteins in neurodegenerative disease is unknown. We sought to determine whether neurodegenerative disease-associated protein aggregates can induce the HSR. Here, we generated a neuroblastoma cell line that expresses a fluorescent reporter under conditions of HSR induction, for example heat shock. Using these cells, we show that the HSR is not induced by exogenous treatment with aggregated forms of Parkinsons disease-associated -synuclein or the ALS-associated G93A mutant of superoxide dismutase-1 (SOD1G93A). Furthermore, flow cytometric analysis revealed that intracellular expression of SOD1G93A or a pathogenic form of polyQ-expanded huntingtin (Htt72Q), similarly, results in no or low induction of the HSR. In contrast, expression of a non-pathogenic but aggregation-prone form of firefly luciferase (Fluc) did induce an HSR in a significantly greater proportion of cells. Finally, we show that HSR induction is dependent on the intracellular levels of the aggregation-prone proteins, but the pathogenic proteins (SOD1G93A and Htt72Q) elicit a significantly lower HSR compared to the non-pathogenic proteins (Fluc). These results suggest that pathogenic proteins either evade detection or impair induction of the HSR in neuronal-like cells. Therefore, defective HSR induction may facilitate the initiation of protein aggregation leading to inclusion formation in neurodegenerative diseases.

cell biology↗

bioRxiv2019

Investigations into the declining health of alder (Alnus glutinosa) along the river Lagan in Belfast, including the first report of Phytophthora lacustris causing disease of Alnus in Northern Ireland

Common alder (Alnus glutinosa) is an important tree species, especially in riparian and wet habitats. Alder is very common across Ireland and Northern Ireland, and provides a wide range of ecosystem services. Surveys along the river Lagan in Belfast, Northern Ireland led to the detection of several diseased Alnus trees. As it is known that Alnus suffers from a Phytophthora induced decline, this research set out to identify the presence and scale of the risk to Alnus health from Phytophthora and other closely related oomycetes. Sampling and a combination of morphological and molecular testing of symptomatic plant material and river baits identified the presence of several Phytophthora species, including Phytophthora lacustris. A survey of the tree vegetation along an 8.5 km stretch of the river revealed that of the 166 Alnus trees counted, 28 were severely defoliated/diseased and 9 were dead. Inoculation studies using potted Alnus saplings demonstrate that P. lacustris was able to cause disease, and Kochs postulates for this pathogen-host combination were completed, which suggests a future risk to Alnus health from P. lacustris in Northern Ireland.

plant biology↗

bioRxiv2019

Arginine valency in C9ORF72 dipolypeptides mediates promiscuous proteome binding that stalls ribosomes, disable actin cytoskeleton assembly and impairs arginine methylation of endogenous proteins

C9ORF72-associated Motor Neuron Disease patients feature abnormal expression of 5 dipeptide repeat (DPR) polymers. Here we used quantitative proteomics in a Neuro2a cell model to demonstrate that the valency of Arg in the most toxic DPRS, PR and GR, drives promiscuous binding to the proteome, compared to a relative sparse binding of the more inert AP and GA. Notable targets included ribosomal proteins, translation initiation factors and translation elongation factors. PR and GR comprising more than 10 repeats robustly stalled the ribosome suggesting high-valency Arg electrostatically jams the ribosome exit tunnel during synthesis. Poly-GR also bound to arginine methylases and induced hypomethylation of endogenous proteins, with a profound destabilization of the actin cytoskeleton. Our findings point to arginine in GR and PR polymers as multivalent toxins to translation as well as arginine methylation with concomitant downstream effects on widespread biological processes including ribosome biogenesis, mRNA splicing and cytoskeleton assembly.\n\nSIGNIFICANCE STATEMENTThe major genetic cause of MND are mutations in an intron of the C9ORF72 gene that lead to the expansion in the length of a hexanucleotide repeat sequence, and subsequent non-AUG mediated translation of the intron into 5 different DPRs. The two DPRs containing Arg are potently toxic in animal and cell models. Our research shows that the valency of Arg mediates widespread proteome binding especially affecting machinery involved in Arg-methylation, cytoskeleton and translation. We suggest the mechanisms for toxicity are multipronged and involve electrostatic jamming of ribosomes during translation, acting as substrate mimetics for arginine methylase activity that renders the endogenous proteome hypomethylated and impairing actin cytoskeleton assembly. These mechanisms explain pathologic signatures previous reported in human brain pathology.

biochemistry↗

bioRxiv2019

ETHYLENE RESPONSE FACTOR (ERF) genes modulate plant root exudate composition and the attraction of plant parasitic nematodes

Plant root exudates are compositionally diverse, plastic and adaptive. Ethylene signalling influences the attraction of plant parasitic nematodes (PPNs), presumably through the modulation of root exudate composition. Understanding this pathway could lead to new sources of crop parasite resistance. Here we have used Virus-Induced Gene Silencing (VIGS) to knockdown the expression of two ETHYLENE RESPONSE FACTOR (ERF) genes, ERF-E2 and ERF-E3 in tomato. Root exudates are significantly more attractive to the PPNs Meloidogyne incognita, and Globodera pallida following knockdown of ERF-E2, which has no impact on the attraction of Meloidogyne javanica. Knockdown of ERF-E3 has no impact on the attraction of Meloidogyne or Globodera spp. GC-MS analysis revealed major changes in root exudate composition relative to controls. However, these changes do not alter the attraction of rhizosphere microbes Bacillus subtilis or Agrobacterium tumefaciens. This study further supports the potential of engineering plant root exudate for parasite control, through the modulation of plant genes.\n\n\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@15fea9dorg.highwire.dtl.DTLVardef@241221org.highwire.dtl.DTLVardef@224609org.highwire.dtl.DTLVardef@24315corg.highwire.dtl.DTLVardef@24953e_HPS_FORMAT_FIGEXP M_TBL C_TBL

plant biology↗

bioRxiv2019

ABC transporters alter plant-microbe-parasite interactions in the rhizosphere

Plants are master regulators of rhizosphere ecology, secreting a complex mixture of compounds into the soil, collectively termed plant root exudate. Root exudate composition is highly dynamic and functional, mediating interactions between plants and a wide range of beneficial / harmful soil organisms. Exudate composition is under selective pressure to diversify in response to pathogen perception, whilst maintaining interactions with beneficial organisms. However, crop domestication has exerted significant and unintended changes to crop root exudate composition, and we know very little about genotype - phenotype linkages that pertain to root exudates and rhizosphere interactions. Better understanding could enable the modulation of root exudate composition for crop improvement by promoting positive, and impeding negative, interactions. Root expressed transporters modulate exudate composition and could be manipulated towards the rational design of beneficial root exudate profiles. Using Virus Induced Gene silencing (VIGS), we demonstrate that knockdown of two root-expressed ABC transporter genes in tomato cv. Moneymaker, ABC-G33 and ABC-C6, alters the composition of semi-volatile compounds in collected root exudates. Root exudate chemotaxis assays demonstrate that knockdown of each transporter gene triggers the repulsion of economically relevant Meloidogyne and Globodera spp. plant parasitic nematodes, which are attracted to control treatment root exudates. Knockdown of ABC-C6 inhibits egg hatching of Meloidogyne and Globodera spp., relative to controls. Knockdown of ABC-G33 has no impact on egg hatching of Meloidogyne spp. but has a substantial inhibitory impact on egg hatching of G. pallida. ABC-C6 knockdown has no impact on the attraction of the plant pathogen Agrobacterium tumefaciens, or the plant growth promoting Bacillus subtilis, relative to controls. Silencing ABC-G33 induces a statistically significant reduction in attraction of B. subtilis, with no impact on attraction of A. tumefaciens. ABC-C6 represents a promising target for breeding or biotechnology intervention strategies as gene knockdown (-64.9%) leads to the repulsion of economically important plant parasites and retains attraction of the beneficial rhizobacterium B. subtilis. This study exposes the link between ABC transporters, root exudate composition, and ex planta interactions with agriculturally and economically relevant rhizosphere organisms, paving the way for an entirely new approach to rhizosphere engineering and crop protection.

plant biology↗

bioRxiv2018

Transcriptional variation and divergence of host-finding behaviour in Steinernema carpocapsae infective juveniles

Steinernema carpocapsae is an entomopathogenic nematode that employs nictation and jumping behaviours to find host insects. We aimed to investigate the transcriptional basis of variant host-finding behaviours in the infective juvenile (IJ) stage of three S. carpocapsae strains (ALL, Breton and UK1). RNA-seq analysis revealed that whilst up to 28% of the S. carpocapsae transcriptome was differentially expressed (P<0.0001) between strains, remarkably few of the most highly differentially expressed genes (>2 log2 fold change, P<0.0001) were from neuronal gene families. S. carpocapsae Breton displays increased chemotaxis toward the laboratory host Galleria mellonella, relative to the other strains. This correlates with the up-regulation of four srsx chemosensory GPCR genes, and a sodium transporter gene, asic-2, relative to both ALL and UK1 strains. The UK1 strain exhibits a decreased nictation phenotype relative to ALL and Breton strains, which correlates with co-ordinate up-regulation of neuropeptide like protein 36 (nlp-36), and down-regulation of an srt family GPCR gene, and a distinct asic-2-like sodium channel paralogue. To further investigate the link between transcriptional regulation and behavioural variation, we sequenced microRNAs across IJs of each strain. We have identified 283 high confidence microRNA genes, yielding 321 isomiR variants in S. carpocapsae, and find that up to 36% of microRNAs are differentially expressed (P<0.0001) between strains. Many of the most highly differentially expressed microRNAs (>2 log2 fold, P<0.0001) are predicted to regulate a variety of neuronal genes that may contribute to variant host-finding behaviours. We have also found evidence for differential gene isoform usage between strains, which alters predicted microRNA interactions, and could contribute to the diversification of behaviour. These data provide deeper insight to the transcriptional landscape of behavioural variation in S. carpocapsae, underpinning efforts to functionally dissect the parasite host-finding apparatus.\n\nAuthor summarySteinernema carpocapsae is a lethal parasite of insects. In order to find and invade a host insect, the S. carpocapsae infective juvenile will typically stand upright, waving its anterior in the air as it searches for host-specific cues. When the infective juvenile senses insect volatile compounds and movement (both signals are required), it will attempt to jump towards the source of those stimuli. Whilst the jumping behaviour is unique to Steinernema species nematodes, nictation is a host-finding behaviour shared with other important parasites of medical and veterinary importance. We have found that different strains of S. carpocpsae use modified host-finding strategies, and that these behavioural differences correlate with gene expression patterns, identifying genes that may be crucial in regulating aspects of host-finding. We also assessed the complement of microRNAs, which are small non-coding RNAs that regulate target gene expression. We found a surprising difference in the abundance of shared microRNAs between strains of S. carpocapsae; these differences also reveal expression differences that correlate with behavioural variation. Predicted microRNA target genes suggest that microRNA variation could significantly influence the behaviour of nematodes. Broadly, this study provides insight to the relationship between gene expression and behaviour, paving the way for detailed studies on gene function.

animal behavior and cognition↗